Single Stranded DNA Aptamers Binding NF-kB/RelA

DNA aptamers are high affinity ligands selected by genetic enrichment techniques to bind to specific protein targets. Because these represent chemically stable and reproducible molecules, they have application as affinity reagents and/or therapeutic drugs to affect the target protein's actions. NF-kB is an important mediator of the innate immune response and mediator of tissue inflammation. Although RNA and double stranded DNA aptamers have been identified to bind to the NF-kB family of proteins, the present invention represents the first identification of single stranded DNA aptamers that recognize NFkB RelA. The aptamers disclosed herein bind to several distinct regions of RelA and may be useful to antagonize the DNA binding of RelA as an inhibitor of cellular inflammation, visualize the location or amount of RelA in tissues from pathological conditions, or to quantitatively measure the activated state of RelA by affinity binding.

METHODS AND COMPOSITIONS FOR DIAGNOSIS OF RICKETTSIA INFECTION

Certain embodiments are directed to detection methods and methods of identifying detection targets for sensitive and specific laboratory tests to diagnose and monitor rickettsial infections during the earliest stages of the disease and to assess the degree of illness. 1rickettsia. A method for detecting and treating acute phase infection comprising:contacting a sample from a subject with antibodies that bind rickettsial protein RC0497 (SEQ ID NO:1) or peptides thereof, wherein one or more antibodies form an antibody complex with RC0497 peptides in the sample;isolating the antibody;detecting the peptides present in the antibody complex; and{'i': 'rickettsia', 'treating the subject identified as having an acute phase infection.'}2. The method of claim 1 , wherein the peptides detected are HDLVGLGEVTVNR (SEQ ID NO:2) claim 1 , LLLSLDSTGEK (SEQ ID NO:3) claim 1 , ELAEAGFGR (SEQ ID NO:4) claim 1 , SDFPAEQIGK claim 1 , (SEQ ID NO:5) claim 1 , EYHNDLTDQAFYAGK (SEQ ID NO:6) claim 1 , EYGYGVESTSTFDQFTQQAVR (SEQ ID NO:7) claim 1 , and/or GASVHYIIDK (SEQ ID NO:8)3. The method of claim 1 , wherein detecting the peptides is by selected reaction monitoring (SRM).4. The method of claim 1 , wherein the antibody is a polyclonal antibody.5rickettsiaR. africae, R. conoriiR. parkeri. The method of claim 1 , wherein the infection is a claim 1 , or infection.6. The method of claim 1 , further comprising detecting at least one host response protein selected from BPI fold-containing family A member 2 claim 1 , Histone H3.3 claim 1 , Ferritin heavy chain claim 1 , 4-hydroxy-phenylpyruvate dioxygenase claim 1 , or Adenylyl cyclase-associated protein 1.7. A polyclonal antibody composition that specifically binds rickettsial protein RC0497 (SEQ ID NO:1).8. The antibody of claim 7 , wherein an epitope bound by the antibody are present on one or more of HDLVGLGEVTVNR (SEQ ID NO:2) claim 7 , LLLSLDSTGEK (SEQ ID NO:3) claim 7 , ELAEAGFGR (SEQ ID NO:4) claim 7 , SDFPAEQIGK claim 7 , (SEQ ID NO:5) ...

Single Stranded DNA Aptamers Binding NF-kB/RelA

DNA aptamers are high affinity ligands selected by genetic enrichment techniques to bind to specific protein targets. Because these represent chemically stable and reproducible molecules, they have application as affinity reagents and/or therapeutic drugs to affect the target protein's actions. NF-kB is an important mediator of the innate immune response and mediator of tissue inflammation. Although RNA and double stranded DNA aptamers have been identified to bind to the NF-kB family of proteins, the present invention represents the first identification of single stranded DNA aptamers that recognize NFkB RelA. The aptamers disclosed herein bind to several distinct regions of RelA and may be useful to antagonize the DNA binding of RelA as an inhibitor of cellular inflammation, visualize the location or amount of RelA in tissues from pathological conditions, or to quantitatively measure the activated state of RelA by affinity binding.

NANOSENSORS AND METHODS FOR DETECTION OF BIOLOGICAL MARKERS

Methods and devices for microfluidic detection of a biological maker in a biospecimen collected from a subject are disclosed. The microfluidic devices include nanoparticle-based nanosensors comprising supramolecular recognition sequences, protease consensus sequences, post-translationally modifiable sequences, or sterically hindered benzylether bonds for specific interaction with a biological marker. Also disclosed are particular nanosensors for detecting cytokines, and other proteins based upon supramolecular recognition without chemical modification or enzymatic cleavage. 1. A method of microfluidic detection of a biological marker in a biological sample collected from a subject , the method comprising: a cartridge and a planar substrate retained in said cartridge, said cartridge comprising a sample inlet well formed in said cartridge above a sample application region in or on said substrate and at least one detection region in fluid communication with said sample application region via a microfluidic channel extending from said sample application region to said detection region, said microfluidic channel having a terminal end positioned distal from said inlet well, and an optional absorbent pad positioned at said terminal end, wherein said detection region comprises a first nanosensor immobilized therein or thereon;', 'wherein said first nanosensor comprises a central carrier particle, a first particle tethered to said carrier particle via an oligopeptide linkage, and a second particle directly attached to said carrier particle, wherein said oligopeptide linkage comprises a supramolecular recognition sequence, a protease consensus sequence, a post-translationally modifiable sequence, or a sterically hindered benzylether bond for specific interaction with a biological marker, wherein at least one of said first and second particles is a detectable particle and the other of said first and second particles is a quencher particle;, 'providing a microfluidic device, ...

Inhibitors of bromodomain-containing protein 4 (brd4)

Certain embodiments are directed to small molecule selective inhibitors of the BRD4 bromodomain. Compounds described herein can be used to modulate the bronchiolar NFkB-BRD4 axis, which plays a role in acute neutrophilic response to viral molecular patterns. Compounds described herein can be developed as preventive and therapeutic agents for various human diseases and conditions.

High affinity mutants of nuclear factor-interleukin 6 and methods of use therefor

The present invention relates to inhibitors of the sequence specific transcription factor nuclear factor IL-6 (NF-IL6) and methods of use therefor. In particular, substitution mutants in the N-terminus of the NF-IL6 tryptic core domain are disclosed that have a higher binding affinity for the DNA binding site than does the wild-type sequence.

Combinatorial selection of oligonucleotide aptamers

A random combinatorial selection method is disclosed for the construction of oligonucleotide aptamers in which nuclease resistance is conferred by the inclusion of modified nucleotides. The modified nucleotides are incorporated during PCR amplification to form achiral modified oligonucleotides. Thio-substituted aptamers are provided that bind tightly to the nuclear factor for human IL6 (NF-IL6).

IKK gamma gene products and methods for making and using same

Disclosed are isolated IKKγΔ; isolated nucleic acid molecules encoding IKKγΔ; expression vectors and cells which contain such nucleic acid molecules; oligonucleotides which are complementary to at least a portion of nucleic acid molecules encoding IKKγΔ but which are not complementary to any portion of nucleic acid molecules encoding wild type IKKγ; antibodies which are specific for IKKγΔ; DNA and RNA oligomers, optionally in labeled or enzymatically active form, which are capable of selectively hybridizing to nucleic acid molecules encoding IKKγΔ; and DNA and RNA oligomers, optionally in labeled or enzymatically active form, which are capable of selectively hybridizing to nucleic acid molecules encoding IKKγΔ but which do not hybridize with nucleic acid molecules encoding wild type IKKγ. Methods for using these materials to inhibit formation of IKKγΔ-containing IKK, to inhibit NF-κB activation, and to treat or prevent inflammation are also disclosed.

Molecular phenotyping of severe asthma

The present invention discloses a method for classifying individuals into those who have airway hyperreactvitiy and those with asthma based on cytokine expression patterns. It is contemplated that such a method will enable rapid identification of individuals requiring intensive treatment for asthma, thereby reducing morbidity and improving quality of life for those affected.

Nanosensors and methods for detection of biological markers

Methods and devices for microfluidic detection of a biological maker in a biospecimen collected from a subject are disclosed. The microfluidic devices include nanoparticle-based nanosensors comprising supramolecular recognition sequences, protease consensus sequences, post-translationally modifiable sequences, or sterically hindered benzylether bonds for specific interaction with a biological marker. Also disclosed are particular nanosensors for detecting cytokines, and other proteins based upon supramolecular recognition without chemical modification or enzymatic cleavage.

Inhibitors of bromodomain-containing protein 4 (brd4)

Certain embodiments are directed to small molecule selective inhibitors of the BRD4 bromodomain. Compounds described herein can be used to modulate the bronchiolar NFkB-BRD4 axis, which plays a role in acute neutrophilic response to viral molecular patterns. Compounds described herein can be developed as preventive and therapeutic agents for various human diseases and conditions.

Inhibitors of bromodomain-containing protein 4 (brd4)

Single stranded DNA aptamers binding NF-kB/RelA

DNA aptamers are high affinity ligands selected by genetic enrichment techniques to bind to specific protein targets. Because these represent chemically stable and reproducible molecules, they have application as affinity reagents and/or therapeutic drugs to affect the target protein's actions. NF-kB is an important mediator of the innate immune response and mediator of tissue inflammation. Although RNA and double stranded DNA aptamers have been identified to bind to the NF-kB family of proteins, the present invention represents the first identification of single stranded DNA aptamers that recognize NFkB RelA. The aptamers disclosed herein bind to several distinct regions of RelA and may be useful to antagonize the DNA binding of RelA as an inhibitor of cellular inflammation, visualize the location or amount of RelA in tissues from pathological conditions, or to quantitatively measure the activated state of RelA by affinity binding.